Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011357.1 Corchorus capsularis cultivar CVL-1 contig11378, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5309
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:1857 original size:30 final size:30

Alignment explanation


    Indices: 1821--1883  Score: 117
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1811 CCCTAAAATT

                                       *  
       1821 AATTTTAAAGTTGTTTATATATTCTTTGAA
          1 AATTTTAAAGTTGTTTATATATTCTTTAAA

                                          
       1851 AATTTTAAAGTTGTTTATATATTCTTTAAA
          1 AATTTTAAAGTTGTTTATATATTCTTTAAA

               
       1881 AAT
          1 AAT

       1884 ATAAGGAAAT


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   32  1.00

ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52


Consensus pattern (30 bp):   
AATTTTAAAGTTGTTTATATATTCTTTAAA

Found at i:4190 original size:29 final size:29

Alignment explanation


    Indices: 4125--4205  Score: 101
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       4115 GCTTAATACC

                                   *        
       4125 CAAATT-AGCCCCTTAACTATTCATTTTGGGA
          1 CAAATTGA-CCCCTTAACT-TT-TTTTTGGGA

                                         
       4156 CAAATTGACCCCTTAACTTTTTTTTGGGA
          1 CAAATTGACCCCTTAACTTTTTTTTGGGA

                   *        *    
       4185 CAAATTGGCCCCTTAAATTTT
          1 CAAATTGACCCCTTAACTTTT

       4206 AAAAAGGAGA


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  29   27  0.59
  30    2  0.04
  31   16  0.35
  32    1  0.02

ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38


Consensus pattern (29 bp):   
CAAATTGACCCCTTAACTTTTTTTTGGGA

Found at i:5054 original size:21 final size:21

Alignment explanation


    Indices: 5028--5071  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5018 GATATCTGGA

                                  
       5028 TTGCTAAAT-ACCGCCCCATTT
          1 TTGCT-AATCACCGCCCCATTT

                  *              
       5049 TTGCTATTCACCGCCCCATTT
          1 TTGCTAATCACCGCCCCATTT

              
       5070 TT
          1 TT

       5072 TACGCTTTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    2  0.10
  21   19  0.90

ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39


Consensus pattern (21 bp):   
TTGCTAATCACCGCCCCATTT
Done.